Human blood is a highly valuable and hitherto indispensable raw material in medicine, which nowadays is used for extracting or manufacturing a large number of components and products. The so-called AIDS scandal in the early 1990s drew sudden public and professional attention to the viral safety of blood and blood products.
Nucleic acid amplification technology (NAT) reduces the risk of infection during blood transfusions.
The risk of becoming infected with viral pathogens such as HIV 1/2, HCV, HBV, or HAV during a blood transfusion has decreased considerably over the past years due to improved analytical methods for blood donations. It has been documented that the introduction of NAT has significantly increased the likelihood of detecting infected blood reserves.
Donor blood must be screened for pathogens before it is administered to a patient. Prior to the introduction of NAT, pathogens such as HIV and hepatitis viruses in blood reserves were primarily identified with antibody detection. Since it takes a certain time for the immune system to form such antibodies in response to an actual infection, these controls were subject to an open time window (diagnostic window). It was impossible to detect pathogens in the corresponding blood donation in the early stages of an infection, which meant that infected blood was able to make its way into medical care. The risk of transfusing infected blood products could only be minimized for therapeutic fresh plasma by asking all blood donors for a second donation, which was given after a minimum interval of 2-3 months. This allowed for detecting the antibodies that had formed in the donor's body in the interim in case of an infection. The originally donated plasma was frozen and could not be used for medical treatment until a second donation had tested negative for the antibody. This approach is not feasible for blood products with a short shelf life of just a few days, such as red blood cells or platelets. In these cases, the product has to be released immediately after donation once it has tested negative. That means the test should show positive results as early as possible in case of a blood donor infection to minimize the diagnostic window. This was accomplished with the introduction of NAT as a screening test for the sensitive direct detection of viral contamination in blood donations.
Successful advances have been made since the mid-1990s in the development of methods to detect viruses based on their nucleic acids. At the suggestion of the plasma-processing industry, which was interested in protecting its production pools for plasma products such as coagulation factor VIII or IX against high virus loads, NAT was introduced in the mid-1990s for the transfusion-relevant viruses HIV-1/2, HCV, and HBV, and later for parvovirus B19 (PB 19) and HAV as quality control measures. In 1999, the Paul Ehrlich Institute (PEI) made HCV NAT testing mandatory for plasma and cellular blood components. The blood donation services of the German Red Cross (DRK) and Bavarian Red Cross (BRK) started using NAT from the beginning, some as early as 1997, to test all donations for the transfusion-relevant viruses HCV, HIV, and HBV. They were also first to expand NAT testing to parvovirus PB 19 and HAV in 2000, which is now standard for all DRK blood donation services. PEI also made HIV-1 NAT mandatory in May 2004.
Thus, some 3.6 million blood donation samples were tested with NAT for HCV and HIV-1 (Roth, W K et al. Transfusion 2002; 42:862-868) and for HBV (Roth, W K et al. Transfusion 2002; 42:869-875) in a study between 1997 and 2002 in Central Europe. This allowed for identifying 6 HCV and 2 HIV-1 PCR-confirmed positive, antibody-negative donations (yield, 1 in 600,000 or 1 in 1.8 million, respectively) as well as 6 HBV PCR-confirmed positive donations that ended up being HBsAg-negative.
Thanks to various measures such as donor selection, ELISA testing and NAT testing, the residual virological risk for the screened transfusion-relevant viruses dropped to a previously unknown, unfathomably low level. Thus, the residual risk in Germany after the introduction of PCR for the three transfusion-relevant viruses HCV, HIV, and HBV is so minimal at below 1:20 million for HCV, below 1:4 million for HIV-1, and below 1:1 million for HBV that one can essentially no longer even refer to a true residual virological risk.
Generally, the introduction of complex and costly NAT led to additional financial burdens for blood donation services. One way to reduce costs is to combine many individual donor samples into a single sample by forming so-called mini-pools (see Roth, W K and Seifried, E, Transfusion Medicine 2002; 12:255-258). This approach particularly benefits large DRK blood donation services with 2,000 to 4,000 donations per day. Testing such a large number of donor samples for currently 6 viruses would require performing up to 24,000 individual NAT tests per day in individual testing. There still are insurmountable technical limitations for carrying out such a large number of individual NAT tests in an 8-hour shift, as neither thermal cyclers/analyzers nor methods exist that would allow for achieving that kind of throughput.
Pooling reduces the number of tests to a technically and financially feasible degree. Up to 96 donor blood samples are combined into a pool, which allows for high sample throughput in a small number of tests (Roth, W K et al. The Lancet 1999; Roth, W K et al. Vox Sang 2000; 78 (suppl 2):257-259).
Nevertheless, even pooled NAT for blood donation testing is still in part a manual procedure, which reduces the immense cost for potentially large sample numbers to an acceptable level, but doesn't yet allow for automating the entire process with pooling and the subsequent steps. That would be a major and important step towards process safety.
Combining donor samples into larger mini-pools may be less beneficial for blood donation services with small to mid-sized donor numbers and for countries with high virus prevalence. If the virus prevalence rises over a specific level, mini-pools that include too many positives—or all mini-pools in the worst case—have to be dissolved and broken down to the positive individual sample. This results in the initial blocking of all samples in these positive pools, including the negative samples. It can therefore take 1-3 days before the blood products represented in the pool are available for application. Accordingly, the concept of creating mini-pools with up to 96 donor blood samples only has limited suitability for NAT testing in countries with high prevalence in the donor collective.
DE 102 58 258 A1 teaches the use of a NAT procedure that achieves very high throughput to meet the needs of large blood donation services. However, it still requires manual interventions.
Combining magnetic particles to which nucleic acids, whether from individual or pooled samples, are bound is generally beneficial. The process can theoretically be continued indefinitely, but in reality, so many beads gather after 3 to 4 steps that the elution of nucleic acids requires increasingly larger buffer volumes, which means that a disadvantageous dilution effect must be accepted with regard to the individual source sample.
The object of the present invention therefore is to develop a method that allows for faster and improved performance of nucleic acid amplification techniques for countries with high prevalence, but also for achieving very high throughput to meet the needs of large blood donation services.
Furthermore, pooling is to no longer impact the test sensitivity by default with regard to individual donations, but has to be equivalent to individual sample testing. This would eliminate a major concern that has been raised about pooling in the past.
The present invention solves this object by providing a method for the—preferably automated—processing of pooled or individual samples. The method comprises the following steps:    a) providing samples to be analyzed in containers, each bearing a machine-readable label,    b) if applicable, combining (pooling) of samples from a) into at least one sample pool in containers, each of which also bears a machine-readable label,    c) adding a solution suited for cellular lysis together with magnetic beads suited for binding nucleic acids to the sample from a) or b),    d) binding the nucleic acids in the sample to the magnetic beads,    e) binding the magnetic beads in the sample to a magnet,    f) pooling the beads from e) by transferring the magnetic particles from at least 2 samples to a new, shared container,    g) repeating steps a) to f) with at least one other set of samples to be analyzed,    h) pooling the beads of the sample pools from steps f) and g) into a shared pool of beads from at least 4 sample pools,    i) repeating steps a) to h) with at least one other set of samples to be analyzed,    j) transferring the beads of the sample pools from steps h) and i) into an at least 8-fold beads pool,    k) eluting the pool from j) with elution buffer, and    l) transferring the eluted nucleic acid from step k) to one or several additional detection methods.
In a preferred embodiment, the method includes one or several wash steps using wash buffer and a magnet.
In a further preferred embodiment, the method allows for combining 2 to 15 and even 30 samples per sample pool in step b), meaning 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 or 15.
Instead of pooled samples, it is also feasible to add individual samples to beads pooling, which achieves the higher sensitivity typical for individual samples with higher throughput.
The present invention solves this object by providing a method for the automated processing of pooled or individual samples as well as for the combination of 2 or more individual samples or sample pools with beads pooling. The method according to the invention leads to increased sample throughput in countries with high prevalence, reduces the time required for sample preparation and processing, and/or enhances the reliability of sample preparation and processing.
The present method avoids the loss of sensitivity with regard to the source sample, since large source volumes may be used, for example in case of individual donations. The pooling effect is still achieved by combining the beads with nucleic acids bound to them into pools of 2, 4, 8 etc.
The nucleic acids are detached from the beads during the elution step and transferred to the detection reaction. Accordingly, 2, 4, 8, . . . n times more beads reach the elution buffer. If the nucleic acid concentration, with reference to individual samples, is not to be changed, the quantity (volume) of the elution buffer must be kept constant and may not be increased accordingly (2-fold, 4-fold, 8-fold etc.). This would increase the bead concentration in the elution buffer, while the available quantity of elution buffer would decrease, since the intermediate space between the beads also doubles, quadruples etc. This is generally considered disadvantageous.
However, it was surprisingly found that this is tolerable. The inventors did not find any sensitivity losses in comparative testing with 2-fold beads pooling and the elution volume only increased slightly up to 4-fold beads pooling.
The fact that the samples themselves can be pooled again increases the throughput, with the known disadvantages of reduced sensitivity, since the individual samples contribute less material to the process depending on the pool size. A current plan presumes a sample volume contribution of 1.5 mL to the process, but also 2.0 mL could be used. This allows for extracting 1.5 mL individual sample volume or, for instance, an individual sample volume of 100 μL in a pool of 15, of 150 μL in a pool of 10, and of 300 μL in a pool of 5. With reference to throughput, sample pooling is multiplied by beads pooling, e.g. to 60 samples per “pool” if pools of 15 samples are combined with 4-fold beads pooling. In conjunction with process length and the number of runs per 8 hours, this results in the maximum throughput per shift.
The method enables users to extract individual donations and/or pools, in parallel if possible, whereby the new platform not only performs beads pooling, but also automatically performs the upstream sample pooling for up to 15 sample pools. This sample pooling, which is performed automatically on the extraction/PCR platform has not been implemented previously and creates essential advantages. Pooling (up to 8-fold based on beads pooling) is made as sensitive as individual donation testing, yet with the added advantage that sample pooling for high throughput can be performed on the same platform, which eliminates the need for separate pooling equipment (as in the state of the art). As with the testing of individual donations, users only load the primary vials of the individual donor, which also only yields one result per donor although pooling was performed (automatically). Users therefore can “forget” about pooling. In case of positive pool results, only the affected individual vials have to be returned to the device to identify the positive individual sample.
In a preferred embodiment, the samples provided for step a) should be liquid or liquefied samples.
The samples preferably are blood samples and other body fluids, particularly whole blood, plasma, serum, cellular blood components and/or other blood products. The blood sample preferably is a sample containing components of the blood. It is preferable to use samples that occur and are used in the blood donation and in transfusion medicine.
This may also include the following blood preparations from whole blood or apheresis donations:                Products of individual donations such as erythrocyte concentrates (EC), platelet concentrates (PC), stem cell preparations, granulocytes or lymphocytes from apheresis, frozen fresh plasma (FFP)        Pooled platelet products such as pool PC from buffy coat        Products from plasma pools such as FFP with SD (solvent/detergent) pathogen inactivation, albumin, clotting factors, fibrin glue, inhibitors, immunoglobulins.        
In a preferred embodiment, steps c), d) and e) of the process can be performed repeatedly.
In a preferred embodiment of the method according to the invention, pooling the blood samples is performed directly in containers labeled with barcodes or in the wells of plates. The method of the present invention effectively eliminates the risk of mixing up samples, which existed with the previous method that involved partial manual steps for virus enrichment. For this purpose, the pooling of blood samples occurs directly in containers labeled with barcodes or in the wells of plates.
In a preferred embodiment, the method according to the invention represents a single homogeneous process without manual intervention.
Preferably, the solution added in step c) consists of reagents for viral lysis such as lysis buffers or combined lysis/binding buffers using detergents, proteases, chaotropic salts, organic solvents or additional solutions and suspensions known to the person skilled in the art, which are suited for extracting nucleic acid, and extraction reagents. Buffers may have alkaline, neutral or acidic pH values. Solid phases for binding the released nucleic acids may be added to the buffers. The solid phases can be paramagnetic, ferrous, uncoated or coated and contain functional groups or not.
In a further preferred embodiment, the samples, and especially blood samples, are screened for the presence of nucleic acid. Nucleic acids preferably are DNA, RNA. Furthermore, the nucleic acid should preferably be that of a virus.
Viruses may be selected from the group consisting of: human immunodeficiency virus 1 and 2 (HIV-1 and HIV-2), as well as HIV-1 subgroups M, N and O, hepatitis C virus (HCV), hepatitis B virus (HBV), cytomegalia virus (CMV, HHV 5), hepatitis A virus (HAV), hepatitis E virus, parvovirus B19 (PB 19), human T cell leukemia virus I/II (HTLV I/II), West Nile virus (WNV), SARS coronavirus (SARS CoV), MERS coronavirus, dengue and other viruses, as well as EBV, HHV 8, HGV/GBVC, TTV or Chikungunya. The method also enables screening for the presence of nucleic acid of previously unknown viruses.
In a preferred embodiment, the method involves simultaneous screening for the presence of nucleic acid from multiple viruses. The method is preferably used for the simultaneous screening for up to 7 viruses such as HCV, WNV, HCMV, HIV-1, HIV-2, HBV, HAV, HEV, and PB 19.
An alternative embodiment may involve screening for free nucleic acids, e.g. those circulating in the plasma. A preferred embodiment of this method uses a large-volume sample of a patient's blood component. The nucleic acids contained therein are subjected to the described method.
The preferred extraction method is lysis with the aid of detergents, binding the released nucleic acids to magnetic particles under acidic conditions, using extraction reagents on the basis of chaotropic salts (as in connection with membranes or magnetic particles as a solid phase) or further extraction methods known to a person skilled in the art.
In a further preferred embodiment, the sample pool(s) is/are prepared for the subsequent amplification step chosen by the user. Preferably, this involves purification of the nucleic acids by binding them to a solid phase, one or several wash steps, and elution of the purified and concentrated nucleic acids.
In particular, the extraction and PCR preparation occurs simultaneously for 7 viruses such as HCV, HIV-1, HIV-2, HBV, HAV, HEV, and PB 19.
A preferred embodiment of the method according to the invention is capable of analyzing 3,780 samples in 8 hours with a maximum pool size of n=15 and at most 4-fold (2-step) beads pooling in 3 runs.
Preferably, 2 to 15 or up to 30 samples are combined per sample pool (step b) of the method. Preferably, the method according to the invention can be used to combine 2, 5, 10, or 15 samples into a sample pool (step a). In a preferred embodiment, 15 samples of 100 μL each, 5 samples of 300 μL each, or 2 samples of 750 μL each can be combined. The preferred total volume of the sample pool is 1.5 mL, optionally 2.0 mL.
The method according to the invention offers advantageously high flexibility for potential scaling up. Accordingly, the source volume of the samples can be increased if higher sensitivity is required. In a preferred embodiment, 15 samples of 100 μL each, 5 samples of 300 μL each, or 2 samples of 750 μL each are used.
Furthermore, the method according to the invention offers the option to increase the sample throughput 2-fold, 4-fold or 8-fold by combining (“beads pooling”) at least 2 sample pools over the course of purification in up to three steps.
In a preferred embodiment of the method, an additional detection procedure consists of nucleic acid amplification. The nucleic acid amplification according to the invention may comprise PCR, TaqMan PCR, real-time PCR, TMA, NASBA, SDA, or LCR.
In a further preferred embodiment, the amplification is followed by a method for the detection of amplified nucleic acids. However, the sample pool may also be subjected to a detection method that does not require prior amplification.
A highly preferred embodiment of the method comprises nucleic acid amplification in the form of real-time PCR, which enables simultaneous online detection of the amplified nucleic acid.
Another aspect of the invention is an apparatus characterized in that it is suited for performing the method according to the invention.
In a preferred embodiment, the apparatus according to the invention is suited for generating sample pools, automatic nucleic acid extraction including beads pooling, PCR preparation, and raw data analysis. An apparatus according to the invention allows for the advantageous linking of the containers in which the sample pools are located, with an automated extraction method.
The apparatus according to the invention comprises several components:                at least one automated pipetting workstation,        at least one magnetic separator,        at least one fluid processing arm, and        at least one robotic arm, and if required and preferred        at least one amplification unit and        at least one detection unit.        
The corresponding components are generally known to the person skilled in the art. The magnetic separator may be integrated into the automated pipetting workstation. A mixing process (e.g. based on pipetting up and down) occurs after adding a liquid (with addition of magnetic solid phases) to the sample pools or individual samples. The liquid is then transferred to reaction vessels via the liquid processing arm on a magnetic separator. Optionally, the magnetic solid phases are transferred to reaction vessels via electromagnets or permanent magnets (“immersion method”). In this step, the magnetic solid phases of 2 sample pools or individual samples, respectively, may be combined in the same reaction vessel by transfer.
In a preferred embodiment of the apparatus according to the invention, all components are designed as an integrated apparatus and are located within housing.
Suitable components for the apparatus according to the invention are, for instance, devices by the Hamilton company of Switzerland. Thus, a suitable automatic pipetting device may consist, for example, of a Hamilton Star or Hamilton Vantage pipettor, while a device, e.g. of the KingFisher type, can serve as a magnetic separator. Devices by other manufacturers such as Tecan, Beckman, Xiril, Sias, ThermoFisher, and Qiagen also are suitable components.
In a further preferred embodiment, the apparatus according to the invention is software-controlled. The extraction process can be controlled with software according to the invention. The monitoring of the entire process (pooling, extraction, beads pooling, detection, evaluation) can be achieved with software. The software monitors the entire process. In this context, the software provides worklists to the software programs of the individual sub-steps and processes, evaluates, and archives, e.g. error messages and sub-step results. The software according to the invention can preferably be programmed to integrate pooling, extraction, beads pooling, PCR preparation and real-time PCR.
Accordingly, a further aspect of the invention comprises a computer program to control and monitor the method according to the invention.
In a further, particularly preferred embodiment, a sample, such as a blood donation sample, is tracked with a barcode label to the final result and is identifiable by that barcode. The direct pooling in containers labeled with barcodes, as well as the automated, barcode-controlled nucleic acid extraction, amplification and detection following the concentration process rule out any mix-up of samples during the entire NAT testing process. Accordingly, the method according to the invention combines the high throughput and the high sensitivities of a method comprising a concentration step with the high safety level of an automated and fully barcode-controlled process.
The method according to the invention effectively eliminates the risk of mixing up samples, which existed with the previous method that involved partial manual steps for virus enrichment. For this purpose, samples, and particularly blood samples, are pooled directly in containers labeled with barcodes. These containers are then transferred to an extraction procedure that does not allow for any sample mix-up due to barcode monitoring or fixed physical allocation. Preferably, this is a fully automated homogeneous process without manual intervention. The extraction process, including beads pooling, is followed by automated and software-monitored PCR setup, amplification, and software-aided detection and evaluation.
Another aspect of the invention relates to the use of an apparatus according to the present invention for the automated processing of pooled or individual samples in accordance with the present invention as described above.
The option of also processing previously pooled samples and of again combining them into larger pools in the specified subsequent process would also be available, including the option to perform this pre-pooling in the same automated equipment. This would also make it feasible in this case to directly load primary vials to the platform without separate pooling devices and to perform automated pre-pooling in the same process.
In case of small blood volume and high prevalence, testing individual samples is the method of choice. In case of larger volumes, combining at least 2 individual samples respectively or forming smaller mini-pools, e.g. 10 or fewer blood donation samples, over the course of the extraction in several subsequent steps is preferred. This method is able to achieve sufficient throughput even with high prevalence. In case of low prevalence, even high-throughput NAT is feasible.
The present invention is further explained in the following examples with reference to the enclosed figures without being limited to the examples.